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Acute myeloid leukemia bearing cytoplasmic nucleophosmin (NPMc+ AML) shows a distinct gene expression profile characterized by up-regulation of genes involved in stem-cell maintenance

Myriam Alcalay, Enrico Tiacci, Roberta Bergomas, Barbara Bigerna, Elisa Venturini, Simone P. Minardi, Natalia Meani, Daniela Diverio, Loris Bernard, Laura Tizzoni, Sara Volorio, Lucilla Luzi, Emanuela Colombo, Francesco Lo Coco, Cristina Mecucci, Brunangelo Falini and Pier Giuseppe Pelicci for the Gruppo Italiano Malattie Ematologiche Maligne dell'Adulto (GIMEMA) Acute Leukemia Working Party

Data supplements

Article Figures & Data

Figures

  • Figure 1.

    Gene-expression profiles of NPMc+ and NPMc AML. (A) Unsupervised hierarchical clustering of the training set. The dendrogram at the top was obtained using a list of 7197 selected genes (see Document S1, available on the Blood website; see the Supplemental Materials link at the top of the online article). The strongest parameter in determining AML clustering is NPM localization. Each of the 39 columns represents an AML sample, and each of the 7197 rows represents a gene (probe set). Genes were clustered according to Pearson correlation (the structure of the gene tree is not shown). (B) Hierarchical clustering of the test set using 369 probe sets obtained from an analysis of variance of the training set (see Document S1). The predictor genes efficiently discriminate AML cases according to NPM localization. Each of the 39 columns represents an AML sample, and each of the 369 rows represents a gene (probe set). Genes were clustered according to Pearson correlation, and the structure of the gene tree is shown. Color scheme used to identify sample characteristics is shown between panels A and B. NK indicates normal karyotype; AK, abnormal karyotype. (C-D) Affymetrix (C) and reverse transcription–quantitative polymerase chain reaction (RT-qPCR) (D) analysis of expression levels of 20 genes (with the highest scores among the 369 predictors) evaluated in 16 patients (8 NPMc+ and 8 NPMc, identified by numbers). (D) Relative expression levels are calculated as deviation from the median, and expression values for each gene in each sample are calculated as 2-ΔCT (ΔCT = difference between the mean threshold cycle for each specific gene and for the 18S control ribosomal RNA gene). In the vast majority of cases, RT-qPCR reflects the results expected from microarray analysis. Homeobox gene expression levels appear to be particularly elevated in NPMc+ AML. The color bar (D, right) represents the color scheme applied to all parts of the figure.

Tables

  • Table 1.

    Main features of the AML cases used for analysis of gene expression profiles

    Patient no.NPM locNPM geneFABFLT3KaryotypeCD34
    Training set
        1 NPMc+ Mut M1 ITD NK Neg
        2 NPMc+ Mut M1 ITD NK Neg
        3 NPMc+ Mut M1 ITD NK Neg
        4 NPMc+ Mut M1 ITD NK Neg
        5 NPMc+ Mut M1 ITD NK Neg
        6 NPMc+ Mut M1 ITD NK Neg
        7 NPMc+ Mut M1 WT NK Neg
        8 NPMc+ Mut M1 WT NK Neg
        9 NPMc+ Mut M1 WT NK Neg
        10 NPMc+ Mut M2 ITD NK Pos
        11 NPMc+ Mut M2 ITD NK Neg
        12 NPMc+ Mut M2 ITD NK Neg
        13 NPMc+ Mut M2 ITD NK Neg
        14 NPMc+ Mut M2 ITD NK Neg
        15 NPMc+ Mut M2 ITD NK Neg
        16 NPMc+ Mut M2 WT NK Neg
        17 NPMc+ Mut M2 WT NK Neg
        18 NPMc+ Mut M2 WT NK Neg
        19 NPMc+ Mut M2 WT NK Pos
        20 NPMc+ Mut M4 ITD NK Neg
        21 NPMc+ Mut M4 ITD NK Neg
        22 NPMc+ Mut M4 WT NK Neg
        23 NPMc+ Mut M4 WT NK Neg
        24 NPMc+ Mut M5a WT NK Neg
        25 NPMc+ Mut M5a WT NK Neg
        26 NPMc+ Mut M5a WT NK Neg
        27 NPMc+ Mut M5b D835 NK Neg
        28 NPMc+ Mut M5b D835 NK Neg
        29 NPMc+ Mut M5b WT NK Neg
        30 NPMc- WT M0 ITD NK Pos
        31 NPMc- WT M0 WT NK Pos
        32 NPMc- WT M1 WT NK Pos
        33 NPMc- WT M1 WT NK Pos
        34 NPMc- WT M1 WT NK Pos
        35 NPMc- WT M2 WT NK Pos
        36 NPMc- WT M4 WT NK Pos
        37 NPMc- WT M4 WT NK Pos
        38 NPMc- WT M5a ITD NK Neg
        39 NPMc- WT M5a ITD NK Neg
    Test set
        40 NPMc+ Mut M1 ITD NK Neg
        41 NPMc+ Mut M1 WT NK Neg
        42 NPMc+ Mut M2 D835 NK Neg
        43 NPMc+ Mut M2 ITD NK Pos
        44 NPMc+ Mut M2 WT NK Neg
        45 NPMc+ Mut M2 WT NK Neg
        46 NPMc+ Mut M4 D835 NK Neg
        47 NPMc+ Mut M4 ITD NK Neg
        48 NPMc+ Mut M4 ITD NK Neg
        49 NPMc+ Mut M4 ITD NK Neg
        50 NPMc+ Mut M4 ITD/D835 NK ND
        51 NPMc+ Mut M4 WT NK Neg
        52 NPMc+ Mut M5 ITD NK Neg
        53 NPMc+ Mut M5a ITD NK Neg
        54 NPMc+ Mut M5a ITD NK Neg
        55 NPMc+ Mut M5a WT NK Neg
        56 NPMc+ Mut M5b ITD NK Neg
        57 NPMc+ Mut M5b ITD NK Neg
        58 NPMc+ Mut M5b WT NK Neg
        59 NPMc+ Mut M5b WT NK Neg
        60 NPMc+ Mut M5b WT NK Neg
        61 NPMc+ Mut M5b WT NK Neg
        62 NPMc+ Mut M0 WT del(11) Pos
        63 NPMc+ Mut M1 WT add(1) Neg
        64 NPMc+ Mut M4 ITD inv(3) Neg
        65 NPMc+ Mut M4 WT tri(8) Pos
        66 NPMc+ Mut M5b ITD del(9) Neg
        67 NPMc+ Mut M5b ITD/D835 tri(8) Neg
        68 NPMc+ Mut M0 WT NK Pos
        69 NPMc- WT M1 ITD NK Neg
        70 NPMc- WT M1 WT NK Pos
        71 NPMc- WT M2 ITD NK Pos
        72 NPMc- WT M2 WT NK Pos
        73 NPMc- WT M2 WT NK Pos
        74 NPMc- WT M4 ITD NK Pos
        75 NPMc- WT M4 ITD NK Pos
        76 NPMc- WT M4 ITD NK Pos
        77 NPMc- WT M4 WT NK Pos
        78 NPMc- WT M4e WT NK Pos
    • NPM loc indicates NPM localization (c+, cytoplasmic and nuclear; c-, nuclear); NPM gene, status of the NPM gene (Mut, mutated; WT, wild type); FAB, M0 to M5 subtypes; FLT3, status of the FLT3 gene (ITD, internal tandem duplication; D835 mutation; WT, wild type); NK, normal karyotype; CD34, immunohistochemical expression of CD34 (Pos, 20% positive blasts; Neg, < 20% positive blasts; ND, no data available).